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United States Patent | 6,214,548 |
Relman ,   et al. | April 10, 2001 |
Nucleic acid-based methods for the detection of Cyclospora are disclosed, including PCR-based and hybridization-based techniques.
Inventors: | Relman; David A. (Palo Alto, CA); Echeverria; Peter (APO AP 96546) |
Assignee: | The United States of America as represented by the Secretary of the Army (Washington, DC); Board of Trustees of Leland Stanford Jr. Univ. () |
Appl. No.: | 015259 |
Filed: | January 29, 1998 |
Current U.S. Class: | 435/6; 435/91.2; 536/23.1; 536/24.3 |
Intern'l Class: | C12Q 001/68; C12P 019/34; C07H 021/02; C07H 021/04; C12N 015/00 |
Field of Search: | 435/6,91.2 536/23.1,24.3,24.32,24.33 935/76,77,78 |
5449768 | Sep., 1995 | Chakraborty et al. | |
5563256 | Oct., 1996 | Chakraborty et al. | 536/24. |
5728526 | Mar., 1998 | George et al. | 435/6. |
5888736 | Mar., 1999 | Lacroix et al. | 435/6. |
Foreign Patent Documents | |||
516385 A1 | ., 1992 | EP. | |
WO 95/00530 | Jan., 1995 | WO. |
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TABLE 1 Primer Sequence (5'.fwdarw.3') SEQ ID NO: Position 1FPL GCGGATCCGCGGCCGCTGGTTGATCCTGCCAGT 3 4-20.sup.a 1520RPL GCGGATCCGCGGCCGCYGCAGGTTCACCTAC 4 1860-1845.sup.a CYCF1E GGAATTCCTACCCAATGAAAACAGTTT 5 418-436.sup.b CYCR2B CGGGATCCAGGAGAAGCCAAGGTAGG 6 1053-1035.sup.b CYCF3E GGAATTCCTTCCGCGCTTCGCTGCGT 7 685-704.sup.b CRCR4B CGGGATCCCGTCTTCAAACCCCCTACTG 8 978-959.sup.b .sup.a underlined bases in primer sequence correspond to indicated positions in Dictyostelium discoideum 17S rRNA (Medlin, et al., 1988).
TABLE 2 Distance Matrix of Small Subunit rDNA Sequence Phylogenetic Dissimilarities (%) Organism Cyc Em Et En Tg Sm Bm Ta Cp Og Gm Dg Cyclospora 4.4 4.0 4.6 Eimeria mitis 2.2 4.0 5.5 Eimeria tenella 1.5 1.1 5.2 Eimeria nieschulzi 2.8 3.1 2.2 Toxoplasma gondii 8.2 8.4 7.7 8.4 Sarcocystis muris 8.0 8.5 7.6 8.0 1.8 Babesia microti 11.9 12.2 11.5 11.8 9.2 9.0 Theileria annulata 11.6 11.9 11.2 11.3 8.6 8.6 5.2 Cryptosporidium 11.9 12.0 11.5 11.8 8.6 8.0 9.0 8.9 parvum Oxytricha 15.5 16.6 16.1 15.8 13.1 13.0 13.8 13.1 11.5 granulifera Glycine max 17.9 18.3 17.3 17.5 15.6 15.1 16.3 15.9 15.0 15.8 Diaphanoeca grandis 15.4 15.8 15.2 15.0 13.8 13.4 14.8 14.2 12.0 13.0 12.6 Saccharomyces 16.8 17.3 16.5 16.8 15.8 15.5 16.9 15.3 14.1 14.4 14.0 9.1 cerevisiae Abbreviations in column headings are same as organisms in left column. Values below diagonal represent phylogenetic dissimilarity scores calculated only with masked positions (1501). Values above diagonal (bold) were calculated using all available (unmasked) small subunit rDNA positions. Only Eimeria sequences could be aligned with the Cyclospora sequence using this more complete set of sequence positions.